#include "command.hpp"
#include "parsimony.h"
#include "treemap.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
-using namespace std;
-
-class GlobalData;
class ParsimonyCommand : public Command {
+
+public:
+ ParsimonyCommand(string);
+ ParsimonyCommand();
+ ~ParsimonyCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "parsimony"; }
+ string getCommandCategory() { return "Hypothesis Testing"; }
+ string getOutputFileNameTag(string, string);
+ string getHelpString();
+ string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
+ string getDescription() { return "generic test that describes whether two or more communities have the same structure"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ FileOutput* output;
+ vector<Tree*> T; //user trees
+ Tree* randT; //random tree
+ Tree* copyUserTree;
+ TreeMap* tmap;
+ TreeMap* savetmap;
+ vector<string> groupComb; // AB. AC, BC...
+ string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile;
+ int iters, numGroups, numComp, counter, processors, numUniquesInName;
+ vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
+ vector< vector<float> > userTreeScores; //scores for users trees for each comb.
+ vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+ EstOutput userData; //pscore info for user tree
+ EstOutput randomData; //pscore info for random trees
+ map<int, double> validScores; //map contains scores from both user and random
+ vector< map<int, double> > rscoreFreq; //map <pscore, number of random trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > uscoreFreq; //map <pscore, number of user trees with that score.> -vector entry for each combination.
+ vector< map<int, double> > rCumul; //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
+ vector< map<int, double> > uCumul; //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+
+ ofstream outSum;
+ bool abort;
+ string groups, itersString;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, string> nameMap;
- public:
- ParsimonyCommand();
- ~ParsimonyCommand() { delete pars; }
- int execute();
+ void printParsimonyFile();
+ int printUSummaryFile();
+ void getUserInput();
+ int readNamesFile();
- private:
- GlobalData* globaldata;
- vector<Tree*> T; //user trees
- Tree* randT; //random tree
- TreeMap* tmap;
- TreeMap* savetmap;
- Parsimony* pars;
- string parsFile, sumFile, distFile, randomtree;
- int iters, numGroups;
- vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
- vector<float> userTreeScores; //scores for users trees
- vector<float> UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
- EstOutput userData; //pscore info for user tree
- EstOutput randomData; //pscore info for random trees
- map<int, float> validScores; //contains scores from both user and random
- map<int, float> rscoreFreq; //pscore, number of random trees with that score.
- map<int, float> uscoreFreq; //pscore, number of user trees with that score.
- map<int, float> rCumul; //pscore, cumulative percentage of number of random trees with that score or lower.
- map<int, float> uCumul; //pscore, cumulative percentage of number of user trees with that score or lower .
- map<int, float>::iterator it;
- map<int, float>::iterator it2;
-
- ofstream out, outSum, outDist;
-
- void printParsimonyFile();
- void printUSummaryFile();
- void getUserInput();
-
};